Seal was eventually arrested in connection with his drug smuggling activities.[3] In a Florida federal court, he was indicted, tried, convicted, and sentenced to 10 years in prison.[3] After his sentencing, Seal approached the DEA and offered to cooperate with the government as an informant.[3] Federal officials agreed to use him as an informant and mentioned his cooperation during hearings in which Seal sought a reduction of his sentence. With an agreement reached, Seal began working as a federal informant in March 1984.[3]

"We made sure all of his aircraft were equipped with the most expensive cryptic radio communications we had ever seen at that time," said DEA Agent Ernest Jacobsen. The operation was very successful and was part of a DEA deal because Seal had been indicted on conspiracy to smuggle Quaalude into Florida in 1984.[4]

In 1988, Jacobsen told a House Judiciary Committee that Seal had flown to an airstrip in Nicaragua in an airplane that had cameras installed by the Central Intelligence Agency.[6] Seal took pictures during the Nicaragua sting operation that purported to show Pablo Escobar, Jorge Luis Ochoa Vásquez, and other members of the Medellín Cartel loading kilos of cocaine onto a C-123 transport plane. Also Frederico Vaughan, whom Seal claimed was an associate of Tomas Borges' of the Interior Ministry of Nicaragua, was photographed with Sandinista soldiers helping load the plane. However, Wall Street Journal reporter Jonathan Kwitney threw strong doubt on Seal's claims of a Sandinista connection: "The Nicaraguan "military airfield" that [US government] officials said Mr. Seal flew from is in fact a civilian field used chiefly for crop-dusting flights, the State Department now concedes. That concession undermines the basis for linking Defense Minister Humberto Ortega, President Ortega's brother, to the operation. In fact, the man who supervised Mr. Seal's work for the government — Richard Gregorie, chief assistant U.S. attorney in Miami — says he could find no information beyond Mr. Seal's word tying any Nicaraguan official to the drug shipment. As for Federico Vaughan, the man Mr. Reagan called an aide to a Sandinista commandant, federal prosecutors and drug officials now say they aren't sure who he is."[7]

Seal was both a smuggler and a DEA informant/operative in this sting operation against the Sandinista government in Nicaragua. In 1984, Seal flew from Nicaragua to Homestead Air Force Base in Florida with a shipment of cocaine that had been allegedly brokered through the Sandinista government.[8] This cocaine was seized by the DEA and was never received by the cartel's distribution handlers in Florida, which immediately caused suspicion in Medellín pointing to Seal as the person responsible for this lost shipment.[9]

A story appeared in the Washington Times in 1984 describing the infiltration of the Medellín cartel's operations in Panama and Nicaragua.[10] The alleged purpose was to prove the Nicaraguan Sandinistas' involvement in the drug trade and to build support for the Contra war effort. This leak and subsequent controversy eventually led to the Iran Contra Affair, which unraveled a year later.[11]

The Wall Street Journal also printed the story. The media coverage indirectly exposed Seal's involvement in the operation. The articles also exposed the Colombian cartel leaders and Nicaraguan Interior Minister who had been photographed moving cocaine onto Seal's aircraft. Despite these pressures, Seal went ahead and testified with the pictures taken during the trip showing Sandinista officials in Nicaragua brokering a cocaine deal with members of Colombia's Medellín Cartel. On March 16, 1986, one month after Seal's death, President Reagan sought to bolster Congressional support for the Contras, by showing on television one of the photographs Seal had taken. He suggested that a top ranking Sandinista official was involved in drug smuggling.[10]

DEA officials in Washington denied the claim a few days later, pointing out that the Nicaraguan was a local fixer.

Cartel member Max Mermelstein testified that he had been instructed in December 1984 either to kidnap Seal and return him to Colombia, or to murder him.[3] The reward to kidnap Seal was $1 million, and the reward to kill him was $500,000.[3]

Seal was sentenced to work in public service at the Salvation Army facility on Airline Highway (U.S. 61) in Baton Rouge, as a modification by the judge to Seal's original plea bargain. On February 19, 1986, Seal was shot to death in front of the site. Seal's shooting abruptly brought the DEA's investigation to an end.

Colombian assassins sent by the Medellín Cartel were apprehended while trying to leave Louisiana soon after Seal's murder. Authorities thus concluded Seal's murderers were hired by Ochoa. The killers were indicted by a state grand jury on March 27, 1986.[12] In May 1987, Luis Carlos Quinter-Cruz, Miguel Velez, and Bernardo Antonio Vasquez were convicted of first degree murder in Seal's death, and sentenced to life in prison without parole.[13]

On March 3, 1986, Louisiana Attorney General William Guste hand-delivered a letter to US Attorney General Edwin Meese criticizing the government's glaring failure to protect Seal as a witness. "In October, as Chairman of the Subcommittee on Narcotics and Drug Interdiction of the President’s Commission on Organized Crime, I had presided over a seminar at which Barry Seal had testified," Guste wrote. "His purpose there was to inform the commission and top United States officials of the methods and equipment used by drug smugglers… and (he) was scheduled to be a key witness in the government’s case against Jorge Ochoa-Vasquez, the head of one of the largest drug cartels in the world. WHY WAS SUCH AN IMPORTANT WITNESS NOT GIVEN PROTECTION WHETHER HE WANTED IT OR NOT?" (all-caps in the original).[14]

Seal is portrayed by Dennis Hopper in the docudramaDoublecrossed (1991),[15] which prominently features Seal's co-pilot and collaborator Emile Camp[16][17] (portrayed by G.W. Bailey), though some of the Camp plotlines stand in for actual events involving William Roger Reeves, who met Seal in jail and introduced him to the Medellin Cartel.[14]

Seal is portrayed by Michael Paré in the American crime drama film The Infiltrator (2016), in two brief scenes which are historically inaccurate, taking dramatic license to depict the film's title character, Robert Mazur, as a passenger in a car being driven by Seal who is killed in a motorcycle drive-by shooting.